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substrates

Valerie Wood val at sanger.ac.uk
Tue Apr 24 05:07:26 PDT 2007


I wonder if anyone has used any of the substrate terms to annotate these 
gene products to 'transporter activity' or its children though?. If so, 
we may not be able to move them directly under "transmembrane 
transporter activity"

We had an idea that we would create some sort of 'transport chaperone' 
under the binding terms which could have the relevent synonyms for 
searching.

I think we were possible even going to have

transporter activity
--transmembrane transorter acrtivity
--transport chaperone (wording and def to be discussed)

protein binding
--transport chaperone

But, as there is no functional relationship between these it probably 
isn't necessary (or correct) to have the
'transporter activity' parentage at all?

One of the probelms we have is that the def of 'transporter activity' is 
quite vague and it doesn't restrict annotations to 'transmembrane 
transport':

Enables the directed movement of substances (such as macromolecules, 
small molecules, ions) into, out of, within or between cells.

It has been used to annotate various other things like  trafficking 
molecules (SNAP receptors, SNAREs),  and various other things. If people 
are agreed that it should never be used for these we could approach this 
slightly differently.

Peter, perhaps you could join the conf call when we deal with this high 
level part?

Val

 

Peter D'Eustachio wrote:

> Hi Jen
>
> Yes - that's how we use them. When we want to talk about the behavior 
> of albumin, we would use a "binding" term.
>
> Peter
>
> ----- Original Message ----- From: "J Clark" <jclark at ebi.ac.uk>
> To: "Peter D'Eustachio" <deustp01 at med.nyu.edu>
> Cc: <transport at genome.stanford.edu>
> Sent: Tuesday, April 24, 2007 6:40 AM
> Subject: Re: substrates
>
>
>> Hi Peter,
>>
>> Thanks, I see what you mean. If I move these terms under the term 
>> 'transmembrane transporter activity' would you be happy with that?
>>
>> Thanks,
>>
>> Jen
>>
>> Peter D'Eustachio wrote:
>>
>>> Narrow answer: No.
>>>
>>> Broad, somewhat tangential answer: yes, maybe. Biologists certainly 
>>> talk about serum albumin and cortisol binding globulin as 
>>> "transporters" of the hydrophobic small molecules that bind to them 
>>> in the blood and thus move from tissue to tissue, but this clearly 
>>> amounts to overloading of the word "transport" as far as we are 
>>> concerned.
>>>
>>> Peter D'Etc
>>>
>>> ----- Original Message ----- From: "J Clark" <jclark at ebi.ac.uk>
>>> To: <transport at genome.stanford.edu>
>>> Sent: Monday, April 23, 2007 10:44 AM
>>> Subject: substrates
>>>
>>>
>>>> Hi,
>>>>
>>>> Can anybody think of any example of transport of the following
>>>> substrates (belonging in the function ontology) that is not
>>>> straightforward transport from one side of a membrane to another?
>>>>
>>>> organic acid transporter activity
>>>> tricarboxylic acid transporter activity
>>>> carbohydrate transporter activity
>>>> alcohol transporter activity
>>>>
>>>> Thanks,
>>>>
>>>> Jen
>>>>
>>>>
>>>>
>>
>> -- 
>> Gene Ontology Consortium
>> EMBL-European Bioinformatics Institute 
>
>
>


-- 
---------------------------------------------------------------------------
Valerie Wood			 Tel: 01223 496909
S. pombe Genome Project		 Fax: 01223 494919 		       
Wellcome Trust Sanger Institute	 email: val at sanger.ac.uk
Wellcome Trust Genome Campus	 http://www.genedb.org/genedb/pombe 
Hinxton, Cambridge, CB10 1HH	 http://www.sanger.ac.uk/Projects/S_pombe




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